The Time Conspiracy
by LadyStar10
Summary: When the Doctor and Clara decide to visit modern day Boston, they accidentally meet Desmond Miles, running from a Templar. However, as they run into the TARDIS, the apple of Eden manages to get stuck in the console, causing the three to travel to the colonial ages and for Desmond to meet an ancestor. However, a trap has been set for Desmond, and only the Doctor can stop it.
1. Prologue: Hi, I'm Desmond!

_**Note: I do not own Assassin's Creed, it belongs to Ubisoft, I also don't own Doctor Who, the BBC does. This is an Assassin's Creed 3 and Doctor Who based fiction. This is rated T due for the cussing , awkward situations, Templars vs. Assassins action, and probably the Doctor acting like himself. I did warn you. Also there's some French language in here since Aveline tends to speak in French sometimes.**_

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_Time and Space, different from each other but for some all the same. There are parts of history never mentioned in school textbooks, or history museums. However, time travelers and those belonging to an order could only remember the secrets themselves encountered. In unexpected times, you can expect friends to come from anywhere and the kind of friends to fall like a leaf into your life._

**Planet: Earth**

**Date: October 2012, unknown date**

**Location: Boston, MA**

Any day in America would start normally, however if you were a time traveler it would start with trouble. On this particular day, everything was different. The Doctor had took Clara to Boston for a weekend vacation. The tourism was normal but not as exciting. Clara seem to only care about taking pictures with her smartphone. The Doctor walked around with her into an historical cemetery in Boston. Some of the graves of the founding fathers were there. Clara took photos of many graves of these famous people. In the midst of it all, the Doctor manage to wander off and leave Clara behind without her noticing. The girl walked towards a different until she manage to almost past a man in a white hood kneeling in front of a grave that had the name of Kenway engraved. The hooded person had a strange gold sphere in his hands and his left arm had very distinctive tattoos. Becoming curious of the stranger, Clara tapped him on the shoulder. The man didn't turn to face her but began to speak.

""If your looking for your guide, the last group left an hour ago." The man said with an American accent. The stranger thought Clara was a lost tourist.

"Oh, I'm not lost; I was just wondering why you're looking upon that grave." Clara corrected and replied to the man. The man finally turned to look at Clara then smiled. The man had signs of shaving stubble on his chin and upper lip, but he also had an visible scar on his face. The man's skin was a dark tan than Clara's own skin and his eyes were a gleaming brown colour.

"Genealogy purposes; It seems one of my ancestors had a part in the American Revolution." The man finally replied. Clara walked closer and began to kneel down towards the grave.

"You're not from around here, are you?" The man asked Clara. Clara smiled and gave her most reasonable answer.

"I'm from London, England actually; I came here with a friend." Clara told the man. The girl turned her head away to see if the Doctor was nearby, but there was no sign of him.

"What is your name miss?" the man asked. Clara turned her head back to face him.

"Clara, Clara Oswald; now aren't you going to tell me yours?" She replied and asked for the man's name. However, the hooded man became very hesitant.

"I rather not say Clara, you see I.." shouts of an police officer from a nearby street interrupted his sentence.

"Found him in the cemetery; I'll approach him quickly." the officer spoke into a communicator on his shoulder. Clara saw the officer runs towards them. Unknown to her, the hooded man grabbed her by the hand and made her run with him.

"Sorry to do this, but there are things you do not know about me." the man said to Clara. The hooded stranger put the gold orb he had earlier in his one shoulder back-pack.

"Wait, why is that policeman after you?" Clara wanted to answer to all the running.

"That officer is after me due to the fact that some maniac told him I was a criminal." the hooded man replied. Clara and himself ran down an empty alley and stopped behind a tall dumpster. They were out of sight for now.

"You still haven't told me your name though!" Clara sort of asked again for a name.

"The name's Desmond Miles, if you're still wondering." Desmond replied. At that moment the officer from earlier had spotted them again. Quickly, Clara grabbed Desmond by the wrist.

"If you want a way to get out of sight, follow me; my friend will help you." Clara offered a chance to escape. The girl and Desmond ran out of the alley and back among the streets. Desmond became curious to who's the friend Clara is referring to. In the distance, a man wearing an purple jacket with a matching bowtie was trying on a bunch of colonial themed hats. Clara now knew that was the Doctor at the hat stand.

"Doctor!" Clara shouted to get his friend's attention. The Doctor turns toward Clara's direction and saw her with a man in a white hoodie. The two were running towards the time traveler and managed to reach him soon enough.

"Clara, sorry I wonder off; had to get a hat for my collection. Oh, I see you made a new friend." The Doctor began to ramble along.

"Doctor, this is no time for fun and games, we need to get to the TARDIS, now." Clara announced. The officer managed to find them but he was not alone, a man in a black hood was with him. The Doctor saw the hooded man was armed with a hidden blade.

"Run!" The Doctor shouted. The three ran at a very quick pace. The unusual strangers pushed some civilians out of the way to reach their destination. The three manage to arrive in front of a blue 1963 British phone box. The officer was out of sight, but the hooded man had to be around the area somewhere.

"Alright then, the sooner we get in, the sooner we can leave." Clara said to Desmond. The assassin couldn't believe the TARDIS was a small phone box.

"In that thing, there is no way we can all fit inside." Desmond said, confusing himself. Out of nowhere, the black hooded assassin appeared and shot an small arrow at the TARDIS. It went pass the Doctor's face before hitting the blue doors. Desmond turned to see the assassin behind them. There was a red cross patched on the mysterious assassin's hoodie. The Doctor noticed the cross was the symbol of the Templar order.

"Desmond Miles, we finally meet at last." the assassin said. In response Desmond wielded his secret blade attached to his right arm.

What do you want?" Desmond asked. The Templar laughed before letting his hood down. The assassin was a blonde man in his early thirties.

"You know what I want from you; give me the apple and I shall spare you and your friends." the villain grinned.

"I'll never do that." Desmond answered. Desmond took off his back-pack and handed it to Clara.

"Protect this with your life; there's something of importance in there." Desmond whispered. He never took his eyes off the Templar. The Templar began to charge at Desmond, beginning the blood thirsty fight to the death. The Doctor quickly opened the TARDIS doors and ushered Clara in.

"Doctor, we need to do something; we can't leave Desmond out there." Clara pleaded for the Doctor to help her new friend. However, the Doctor was more concern on what was in the back-pack that was so important.

"Clara, I need you to open that bag and take whatever may seems strange enough for anyone to steal." The Doctor commanded. Immediately, Clara did as she was told and unzipped the bag. She shuffled and took out many things out of the bag. Including a smart phone, a pair of headphones, a weapon of some sort, a map of Boston, then she found what was stranger then all the things found. She manage to find the golden orb, the same orb Desmond had earlier in his hands. The Doctor saw the object in her hands and was surprise he was actually looking at the original Apple of Eden. The fight outside manage to get inside the TARDIS. The Templar saw Clara had the apple in her hands. The man ran towards her and manage to grab her with one of her arms pinned behind her back and a blade near her throat.

"Hand me the apple girly, and I'll let you live." the man rudely told Clara. The Doctor took out his sonic screwdriver and pointed it at the man.

"Let her go, we do not want to get involve in this business of yours." The Doctor demanded the man to let go of his friend.

"Or what, that sonic device won't harm me." The Templar laughed. Behind him, Desmond tiptoed closer to him, with a his blade ready to be used. The Doctor knew an surprised assassination must be done since there was no option left.

"Now, do as you're told and I'll let you.." The man stopped talking and then gasped in pain. Desmond had successfully stabbed him in the lung.

"You should of listened to the man in the bow tie." Desmond said his version of an goodbye to the Templar. The Templar assassin fell on the ground, dragging Clara along the fall. The apple of Eden flew out of her hands and onto the TARDIS console. The Doctor tried his best to catch it before it got in contact with the console. It was too late, and the apple of Eden landed. Suddenly the apple began to glow, along with the TARDIS, light emitted inside the blue box. The TARDIS glowed around the three and the dead Templar. Just as the Doctor had predicted, the Apple was being connected to the TARDIS. Not even good could come out of what was going to happen next. The engines of the time machine started. The dead body of the Templar was somehow disposed off. Desmond rushed towards the doors, only to find them locked. Clara got on her feet and manage to hang on to a railing.

"Doctor, what's happening?" She asked. The Doctor walked towards the console to see if anything could give an answer to the TARDIS behaving after being connected to the Apple.

"We seem to be going through the time vortex, the Apple had manage to attach itself to the console and is driving the TARDIS." The Doctor answered. In surprise, Desmond ran towards the console and tried to pry away the apple, but the apple was attached on there good.

"It won't unattached!" Desmond said. The TARDIS shook with much monstrosity. Clara had to use her legs along with her arms to kept herself holding on to the railing.

"Hold on tight, we're going to have a rough landing." The Doctor commanded. The TARDIS flew violently until it manage to land with a loud boom. That destination was the colonial Davenport community near Boston. Home of one of Desmond's ancestors.

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**Okay, what did you think of my attempt at a Doctor Who/ Assassin's Creed crossover, read and review please. I want to know what you think,**


	2. Chapter 1:Explosion Of Something New

_**Note: I do not own Assassin's Creed, it belongs to Ubisoft, I also don't own Doctor Who, the BBC does. This is an Assassin's Creed 3 and Doctor Who based fiction. This is rated T due for the cussing, awkward situations, Templars vs. Assassin action, and probably the Doctor acting like himself. I did warn you. Also there's some French language in here since Aveline tends to speak in French sometimes.**_

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Everyone inside the blue box had their backs to the floor from the impact. Desmond was the first to sit up quickly after the crash. He began to rub the back of his head since it ached.

"What the hell happened?" the modern assassin asked. Clara grabbed a hold of one of the railings to pull herself to her feet. Her eyes wandered around the room for the Doctor. The Doctor was on his knees in front of the console. His eyes were directly on the apple of Eden.

"Doctor, do you know where we've landed?" Clara asked. The Doctor quickly stood up and took out his sonic screwdriver. As always, he scanned the room around him. No answer didn't seem to come quick enough.

"I'm not sure?" The time lord replied. Desmond stood on his feet and walked over to one of the screens on the console. The location and time era displayed in words, giving the assassin an answer.

"Wait, this thing can time travel?" The Doctor turned his head to face the assassin before running towards the screen. The time and date was displayed perfectly, revealing there were in the Colonial ages. The location displayed showed they were still in America, but a few miles from colonial Boston.

"Well, at least were almost in a place familiar." The Doctor made a horrible joke. Clara rolled her eyes in response.

"If you two don't tell me where the hell we are, I'll go find out outside." Clara said. She quickly ran towards the doors to open them. Desmond and The Doctor turned around to stop her.

"Wait, it may not be safe out…" It was already too late for Desmond to finish his plea. Clara opened the TARDIS doors letting in bright sunlight. The light blinded them at first but their eyes soon adjusted. Clara already disappeared outside. Desmond and The Doctor hurried out of the TARDIS to catch up to her. When they got out into the wilderness, they notice the TARDIS had landed near a small colonial community. To Desmond, the community seems familiar.

"Doctor, you said we were far from Boston, how far from Boston?" Desmond asked. The Doctor turned towards the assassin.

"Depends, if you take carriage or a short ship ride." the time lord replied. Desmond's mind wandered with some memories from inside the animus. It was all coming back to him. This was the Davenport community where the assassin brotherhood resided in the colonial ages, and where one of his ancestors lived. Desmond's mind soon stopped bringing up memories when the Doctor reminded him that Clara walked away without them.

"We better not dilly dally, we must find Clara." The Doctor grabbed Desmond by the arm and led the way through the village. The two men manage to pass some citizens, some of them giving the unknown strangers a weird look.

"Doctor, are you sure it's a good idea to walk through here?" Desmond asked, getting tangled nerves.

"I'm sure, I used to the thrills already." The time lord spoke like a mad man. Desmond looked at his surroundings carefully.

"I think we should turn back, and wait for Clara to come back." Desmond said. His assassin like instincts started to kick in.

"Nonsense Desmond, the girl can't handle herself alone out her, however she did rescue a planet with a leaf." The Doctor wandered into thought. Desmond rolled his eyes in response. At that moment, the men came across a tavern.

"Maybe she's in there?" Desmond said, wanting to get away from the outside world. The Doctor turned his head and look at the tavern.

"We'll she was a barmaid once, it wouldn't surprise me." The Doctor said. The time lord turned his body and began to walk towards the white tavern. The Doctor came towards the entrance and opened the door. Both he and Desmond walked in. A fire was blazing in the fireplace, warming up the place. A middle age barmaid was serving beer to men who chatting up a storm. There was no sign of Clara in the place.

"The only barmaid I see is that woman, but no Clara." The Doctor deducted. Desmond let his eyes wander for a bit. Some of the men seem to be seamen or even lumberjacks. Desmond could recognize some of them as friends of his ancestor.

"Well since we're hear, how about we buy a drink." Desmond suggested.

"Suit yourself, I don't drink alcohol much, taste boring." The Doctor responded. One of the seamen hears the Doctor's words.

"Boring, ye call beer boring, let me tell ye lad that it 'nun' boring." A grey haired man said. Desmond recognized the seaman as Robert Faulkner, who just spoke.

"Forgive my friend, he's new around here." Desmond said to the sailor. One of the lumberjacks spoke up.

"You two look new around these parts, where did you come from anyway." a red head lumberjack said. Desmond became silent to answer.

"He's from New York, I'm just from England." The Doctor said. Some of the men stood up in response to the Doctor's answer.

"You better not be one of those loyalist." one of the other seamen said.

"Loyalist, to that idiot on the throne, never." The Doctor replied. The men became silent then laughed.

"Good one; from the man in the odd chaps." one of the men said. Desmond made a quick fake laugh with the men of the bar. The Doctor looked at his own clothing in response.

"What's wrong with my clothes; bow ties are cool?" The Doctor said becoming a little offended by the remark. The laughter continued for a while until someone walked in behind the Doctor and Desmond. Desmond hears the door close behind him and slightly turned his head. Behind him was a man in white colonial assassin robes and moccasins covering his legs and feet? Desmond pulled the Doctor by the arm and the two stepped out of the man's way. Robert Faulkner's laughter died down once he spotted the man.

"Connor, we're just having a conversation to these newcomers before ye came; The British speaking' one can make us laugh up a storm." Faulkner made a small laugh. Connor pulled down his hood before he spoke.

"Sorry to interrupt your fun Faulkner, but we got a situation at the docks." Connor said. Faulkner and the rest of the seamen put down their drinks in response. Connor walked back outside, not before he caught a quick glimpse of both the Doctor and Desmond standing near the door. Desmond looked back at Connor before the seamen followed after their captain. The bar was now empty except for the barmaid and the two time travelers still inside. Clara walked in the bar a minute later with some exhaustion.

"There you two are where you were?" She asked. Desmond raised a brow at her.

"What do you mean where were we, we were looking for you since you wandered off from that blue time traveling box." Desmond said, trying to correct her. Clara walked over towards them.

"My apologies but while I walked away from the TARDIS, I manage to witness part of a shipping port explode. Odd enough a silver rat thing seems to crawled out of one of the shipping crates near the port." The Doctor's eyes went wide in response. Quickly, the Doctor began to storm out the door. Desmond and Clara only stop in surprise.

"Where the hell are you going, I've just found you Doctor?" Clara said. Desmond took the woman by the hand and began to follow after the Doctor.

"No time to argue lady, we better catch up to him." the modern assassin said dragging Clara along the way. Two minutes later, the three reached the dock where the Aquila and two other ships were tied. The Aquila only had minor damage, but one of the other ships was on fire. Some of the seamen and other villagers were putting out the fire with buckets of water. Connor stood near some of the damaged debris, carefully, examines every piece.

"What was the cargo of this ship Faulkner?" Connor asked the first mate a question.

"Unknown, we suspect it to be imported fabrics, but it might as well be gunpowder." Faulkner said. To the Doctor the crime scene seemed a little off than a normal one. The mentioning by Clara of a silver rat being near the area could only mean the culprit wasn't human. The Doctor took out his sonic screwdriver and the wallet that contained the psychic paper. Desmond saw what the Doctor took out of his jacket.

"Doctor, what do you plan to do?" Desmond whispered.

"Follow my lead Desmond and I'll show you." The doctor replied. The Doctor flipped open the wallet revealing a blank paper. To Desmond it was blank, or so he thought.

"Everyone out of the way, I need to see the crime scene for evidence." The Doctor shouted with the psychic paper in hand. Many colonist moved out of his way, Desmond could only follow him just in case the Doctor's suppose plan backfired. The Doctor walked towards Connor before putting the psychic paper back in his jacket.

"Hello there, I and my friends were just passing through and we heard there was an explosion here; so I thought I should investigate since me and my assistants tend to work in cases like this." The Doctor began to babble on. Desmond could only think the worst reply Connor would use towards the Doctor. Apparently, it wasn't a reply Desmond was expecting.

"Are you a detective by any chance?" Connor asked. Clara stepped in abruptly.

"Yes he is the best from England my friend." Clara added to the Doctor's lie.

"Then maybe you can help me find out what was involved in the explosion." Connor replied. Desmond raised a brow at The Doctor as the time lord began to smile in victory.

"You're completely mad Doctor." Desmond said in a whisper.

"You'll get used to it." Clara whispered to Desmond. The three followed Connor near an crate that wasn't damaged.

"My men haven't opened this one to see what is still intact; how about one of your assistants opens it for," Connor suggested looking up at Desmond. The Doctor turned towards the assassin with a smile.

"Desmond, will you do the honors." The Doctor said. Desmond reluctantly approached the crate and started to wield his hidden blade. He used the end of the blade to pry the lid open. Connor was watching Desmond's every move. The crate opened a minute later, revealing there were only empty sacs.

"That's odd; there are only empty sacs in this one." Desmond said. The Doctor kneel towards the ground and pointed his sonic screwdriver inside of the crate.

"That is strange, however there's seems to be a strange signature of metal in here." The Doctor extended his loose hand into the box and pulled out a little sheet of metal. It was very odd piece of metal, especially one to be found in a wooden crate.

"Whatever you were shipping was only worth two in the bush for many, but for someone worth more than their humanity." The Doctor spoke. The seamen around them began to groan in response.

"We got cheated out of trade, how dare those traders." one of the seamen said. The contents in the crate still didn't solve what cause the explosion in the first place.

"I better look into this further, do you mind if we stay in town for a while." The Doctor said towards Connor.

"Not at all, you seem to entertain the men earlier as well help me to figure out a piece of the puzzle of what happened to one of the ships." Connor said in reply. Desmond could only give a face palm in response. For some reason, the modern day assassin knew this was going to be a long stay.

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**So, what do you think of Chapter 1 so far, I think I might make Desmond a love interest to Clara, if that's okay with you readers. Read and Review please, I need some suggestions for the next chapter.**


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